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You searched for: subject:"genetics"
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[audio]Good Health
terms
Keywords: Genetics
Downloads: 2
[audio]Genetics 11/10
Genetics lecture on November 10, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 28
[audio]Genetics 10/13
Genetics lecture on October 13, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 62
[audio]Genetics 11/21
Genetics lecture on November 21, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 31
[audio]Genetics Lecture 7, 9/12: Review for Test 1
Genetics Lecture 7, 9/12: Review for Test 1 with Dr. Schau at North Park University.
Keywords: genetics
Downloads: 67
[audio]Genetics 9/22
Genetics lecture with Dr. Schau at North Park University on September 22, 2008 discussing linkage mapping in Eukaryotes. http://genetics3210.blogspot.com/
Keywords: genetics
Downloads: 30
[texts]Report of the third international conference 1906 of genetics (Volume 3rd 1906)

Keywords: genetics
Downloads: 54
[texts]Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences - Sebastian Lippold
To investigate in detail the paternal and maternal demographic histories of humans, we obtained ~500 kb of non-recombining Y chromosome (NRY) sequences and complete mtDNA genome sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). Our results: confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA; suggest very small ancestral effective population sizes (
Keywords: Genetics
Downloads: 1
[texts]Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates - Chuan-Chao Wang
We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R...
Keywords: Genetics
Downloads: 1
[texts]Cell specific eQTL analysis without sorting cells - Harm-Jan Westra
Expression quantitative trait locus (eQTL) mapping on tissue, organ or whole organism data can detect associations that are generic across cell types. We describe a new method to focus upon specific cell types without first needing to sort cells. We applied the method to whole blood data from 5,683 samples and demonstrate that SNPs associated with Crohns disease preferentially affect gene expression within neutrophils.
Keywords: Genetics
Downloads: 1
[audio]Genetics 9/29
Genetics lecture on September 29, 2008 at North Park University with Dr. Schau. Lecture covered primary sexual differentiation, genetic diseases and dosage compensation
Keywords: genetics
Downloads: 21
[texts]The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia - Bayazit Yunusbayev
The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia...
Keywords: Genetics
Downloads: 4
[texts]Efficient Bayesian mixed model analysis increases association power in large cohorts - Po-Ru Loh
Linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. However, existing methods are computationally intractable in large cohorts, and may not optimize power. All existing methods require time cost O(MN^2) (where N = #samples and M = #SNPs) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power...
Keywords: Genetics
Downloads: 2
[texts]When genomes collide: multiple modes of germline misregulation in a dysgenic syndrome of Drosophila virilis - Mauricio A. Galdos
In sexually reproducing species the union of gametes that are not closely related can result in genomic incompatibility. Hybrid dysgenic syndromes represent a form of genomic incompatibility that can arise when transposable element (TE) abundance differs between two parents. When TEs lacking in the female parent are transmitted paternally, a lack of corresponding silencing small RNAs (piRNAs) transmitted through the female germline can lead to TE mobilization in progeny...
Keywords: Genetics
Downloads: 3
[texts]Dead or just asleep? Variance of microsatellite allele distributions in the human Y-chromosome. - Joe Flood
Several different methods confirm that a number of micro-satellites on the human Y-chromosome have allele distributions with different variances in different haplogroups, after adjusting for coalescent times. This can be demonstrated through both heteroscedasticity tests and by poor correlation of the variance vectors in different subclades. The most convincing demonstration however is the complete inactivity of some markers in certain subclades – “microsatellite death”, while they are sti...
Keywords: Genetics
Downloads: 5
[texts]Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis - Bethann S Hromatka
Roughly one in three individuals is highly susceptible to motion sickness and yet the underlying causes of this condition are not well understood. Despite high heritability, no associated genetic factors have been discovered to date. Here, we conducted the first genome-wide association study on motion sickness in 80,494 individuals from the 23andMe database who were surveyed about car sickness. Thirty-five single-nucleotide polymorphisms (SNPs) were associated with motion sickness at a genome-wi...
Keywords: Genetics
Downloads: 5
[texts]Spatial localization of recent ancestors for admixed individuals - Wen-Yun Yang
Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over non-model-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum...
Keywords: Genetics
Downloads: 5
[texts]Differential relationships between habitat fragmentation and within-population genetic diversity of three forest-dwelling birds - Benjamin Zuckerberg
Habitat fragmentation is a major driver of environmental change affecting wildlife populations across multiple levels of biological diversity. Much of the recent research in landscape genetics has focused on quantifying the influence of fragmentation on genetic variation among populations, but questions remain as to how habitat loss and configuration influences within-population genetic diversity. Habitat loss and fragmentation might lead to decreases in genetic diversity within populations, whi...
Keywords: Genetics
Downloads: 6
[texts]Cosi2 : An efficient simulator of exact and approximate coalescent with selection - Ilya Shlyakhter
Motivation: Efficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection...
Keywords: Genetics
Downloads: 4
[audio]Genetics 9/5
Genetics lecture 9/5 with Dr. Schau. Trihybrid crosses.
Keywords: genetics
Downloads: 93
[texts]Cross-population Meta-analysis of eQTLs: Fine Mapping and Functional Study - Xiaoquan Wen
Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at the molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistently presented across populations, accounting for population heterogeneity in allele frequencies a...
Keywords: Genetics
Downloads: 5
[texts]Behavioral individuality reveals genetic control of phenotypic variability - Julien F Ayroles
Variability is ubiquitous in nature and a fundamental feature of complex systems. Few studies, however, have investigated variance itself as a trait under genetic control. By focusing primarily on trait means and ignoring the effect of alternative alleles on trait variability, we may be missing an important axis of genetic variation contributing to phenotypic differences among individuals. To study genetic effects on individual-to-individual phenotypic variability (or intragenotypic variability)...
Keywords: Genetics
Downloads: 9
[texts]Robust Population Structure Inference and Correction in the Presence of Known or Cryptic Relatedness - Matthew P Conomos
Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multi-dimensional scaling (MDS), and model-based methods for proportional ancestry estimation...
Keywords: Genetics
Downloads: 8
[texts]Mixed Model with Correction for Case-Control Ascertainment Increases Association Power - tristan hayeck
We introduce a Liability Threshold Mixed Linear Model (LTMLM) association statistic for ascertained case-control studies that increases power vs. existing mixed model methods, with a well-controlled false-positive rate. Recent work has shown that existing mixed model methods suffer a loss in power under case-control ascertainment, but no solution has been proposed. Here, we solve this problem using a chi-square score statistic computed from posterior mean liabilities (PML) under the liability th...
Keywords: Genetics
Downloads: 12
[texts]Heteroplasmy is ubiquitous and stable at the single cell level - Anitha D Jayaprakash
Eukaryotic cells carry two genomes, nuclear (nDNA) and mitochondrial (mtDNA), which are ostensibly decoupled in their replication, segregation and inheritance. It is increasingly appreciated that heteroplasmy, the occurrence of multiple mtDNA haplotypes in a cell, plays an important biological role, but its features are not well understood. Until now, accurately determining the diversity of mtDNA has been difficult due to the relatively small amount of mtDNA in each cell ( 98%) mtDNA and its abi...
Keywords: Genetics
Downloads: 2
[texts]Variational Inference of Population Structure in Large SNP Datasets - Anil Raj
Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, a...
Keywords: Genetics
Downloads: 4
[texts]Conditions for the validity of SNP-based heritability estimation - James J Lee
The heritability of a trait ($h^2$) is the proportion of its population variance caused by genetic differences, and estimates of this parameter are important for interpreting the results of genome-wide association studies (GWAS). In recent years, researchers have adopted a novel method for estimating a lower bound on heritability directly from GWAS data that uses realized genetic similarities between nominally unrelated individuals...
Keywords: Genetics
Downloads: 6
[texts]The overdue promise of short tandem repeat variation for heritability. - Maximilian Press
Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. Here, we review the promise of STRs in contributing to complex trait heritability, and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single nucleotide variants to have epistatic interacti...
Keywords: Genetics
Downloads: 9
[audio]Genetics 10/1
Genetics lecture on October, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 42
[texts]Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms - Fernando Racimo
Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution, disease genetics and the maintenance of variation genome-wide. Here, we develop an approximation to the distribution of fitness effects (DFE) of segregating single-nucleotide mutations in humans. Unlike previous methods, we do not assume that synonymous mutations are neutral or not strongly selected, and we do not rely on fitting the DFE of all new n...
Keywords: Genetics
Downloads: 8
[texts]Genetic influences on translation in yeast - Frank W. Albert
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosome profiling to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes...
Keywords: Genetics
Downloads: 5
[texts]The conserved PFT1 tandem repeat is crucial for proper flowering in Arabidopsis thaliana - Pauline Rival
It is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in the Arabidopsis thaliana gene PFT1 (MED25), where it encodes an interrupted polyglutamine tract...
Keywords: Genetics
Downloads: 6
[texts]Human genetics and clinical aspects of neurodevelopmental disorders - Gholson J Lyon
There are ~12 billion nucleotides in every cell of the human body, and there are ~25-100 trillion cells in each human body. Given somatic mosaicism, epigenetic changes and environmental differences, no two human beings are the same, particularly as there are only ~7 billion people on the planet. One of the next great challenges for studying human genetics will be to acknowledge and embrace complexity...
Keywords: Genetics
Downloads: 7
[texts]Reconstructing Austronesian population history in Island Southeast Asia - Mark Lipson
Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the "Austronesian expansion," which began 4-5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow...
Keywords: Genetics
Downloads: 6
[texts]The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20 - Morgan Price
Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible...
Keywords: Genetics
Downloads: 19
[texts]Estimating strength of polygenic selection with principal components analysis of spatial genetic variation - Davide Piffer
Principal components analysis on allele frequencies for 14 and 50 populations (from 1K Genomes and ALFRED databases) produced a factor accounting for over half of the variance, which indicates selection pressure on intelligence or genotypic IQ. Very high correlations between this factor and phenotypic IQ, educational achievement were observed (r>0.9 and 0.8), also after partialling out GDP and the Human Development Index...
Keywords: Genetics
Downloads: 10
[texts]Efficient site-specific editing of the C. elegans genome - Donglei Zhang
In just two years, genome editing with the CRISPR-associated endonuclease Cas9 has transformed genetic analysis in conventional and emerging model organisms. The efficiency of this method varies among systems and continues to be optimized. Numerous strategies have been reported for editing the C. elegans genome. To date, these strategies do not provide a simple, rapid and inexpensive means to introduce and isolate arbitrary point mutants...
Keywords: Genetics
Downloads: 10
[texts]Sharing of Very Short IBD Segments between Humans, Neandertals, and Denisovans - Gundula Povysil
We analyze the sharing of very short identity by descent (IBD) segments between humans, Neandertals, and Denisovans to gain new insights into their demographic history. Short IBD segments convey information about events far back in time because the shorter IBD segments are, the older they are assumed to be. The identification of short IBD segments becomes possible through next generation sequencing (NGS), which offers high variant density and reports variants of all frequencies...
Keywords: Genetics
Downloads: 7
[audio]Genetics 10/8
Genetics lecture on October 8, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 45
[texts]A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry - Aram Yardumian
The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportations during the Roman conquest of Palestine, as well as migration from Babylonia, and eventual settlement along the Rhine...
Keywords: Genetics
Downloads: 17
[texts]The genetic ancestry of African, Latino, and European Americans across the United States. - Katarzyna Bryc
Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans brought largely by the Trans-Atlantic slave trade, shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americ...
Keywords: Genetics
Downloads: 17
[texts]Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function - John F Mulley
Background Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles, although the lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancre...
Keywords: Genetics
Downloads: 10
[texts]Genomic and transcriptomic insights into the regulation of snake venom production - Adam D Hargreaves
The gene regulatory mechanisms underlying the rapid replenishment of snake venom following expenditure are currently unknown. Using a comparative transcriptomic approach we find that venomous and non-venomous species produce similar numbers of secreted products in their venom or salivary glands and that only one transcription factor (Tbx3) is expressed in venom glands but not salivary glands. We also find evidence for temporal variation in venom production...
Keywords: Genetics
Downloads: 17
[texts]ESTIMATION OF (CO)VARIANCE COMPONENTS BY WEIGHTED AND UNWEIGHTED SYMMETRIC DIFFERENCES SQUARED, AND SELECTED MIVQUE'S: RELATIONSHIPS BETWEEN METHODS AND RELATIVE EFFICIENCIES - John W Keele
PhD dissertation, Ohio State University
Keywords: genetics
Downloads: 113
[texts]Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth - Fabien Delahaye
Extreme fetal growth is associated with increased susceptibility to a range of adult diseases through an unknown mechanism of cellular memory. We tested whether heritable epigenetic processes in long-lived CD34+ hematopoietic stem/progenitor cells (HSPCs) showed evidence for re-programming associated with the extremes of fetal growth. Here we show that both fetal growth restriction and over-growth are associated with global shifts towards DNA hypermethylation, targeting cis-regulatory elements i...
Keywords: Genetics
Downloads: 17
[texts]Non-crossover gene conversions show strong GC bias and unexpected clustering in humans - Amy L. Williams
Although the past decade has seen tremendous progress in our understanding of fine-scale recombination, little is known about non-crossover (or "gene conversion") resolutions. We report the first genome-wide study of non-crossover gene conversion events in humans. Using SNP array data from 94 meioses, we identified 107 sites affected by non-crossover events, of which 51/53 were confirmed in sequence data...
Keywords: Genetics
Downloads: 11
[texts]Genetics - Herskowitz, Irwin Herman, 1920-
Includes bibliographical references
Keywords: Genetics
Downloads: 5,561
[texts]Genetic dissection of MAPK-mediated complex traits across S. cerevisiae - Sebastian Treusch
Signaling pathways enable cells to sense and respond to their environment. Many cellular signaling strategies are conserved from fungi to humans, yet their activity and phenotypic consequences can vary extensively among individuals within a species. A systematic assessment of the impact of naturally occurring genetic variation on signaling pathways remains to be conducted. In S. cerevisiae , both response and resistance to stressors that activate signaling pathways differ between diverse isolate...
Keywords: Genetics
Downloads: 5
[texts]Regulatory variants explain much more heritability than coding variants across 11 common diseases - Alexander Gusev
Common variants implicated by genome-wide association studies (GWAS) of complex diseases are known to be enriched for coding and regulatory variants. We applied methods to partition the heritability explained by genotyped SNPs (h2g) across functional categories (while accounting for shared variance due to linkage disequilibrium) to genotype and imputed data for 11 common diseases. DNaseI Hypersensitivity Sites (DHS) from 218 cell-types, spanning 16% of the genome, explained an average of 79% of ...
Keywords: Genetics
Downloads: 28
[texts]Hierarchical Bayesian model of population structure reveals convergent adaptation to high altitude in human populations - Matthieu Foll
Detecting genes involved in local adaptation is challenging and of fundamental importance in evolutionary, quantitative, and medical genetics. To this aim, a standard strategy is to perform genome scans in populations of different origins and environments, looking for genomic regions of high differentiation. Because shared population history or population sub-structure may lead to an excess of false positives, analyses are often done on multiple pairs of populations, which leads to i) a global l...
Keywords: Genetics
Downloads: 6
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